Align Fructose import permease protein FrcC (characterized)
to candidate WP_011842126.1 RSPH17029_RS15860 ABC transporter permease
Query= SwissProt::Q9F9B1 (360 letters) >NCBI__GCF_000015985.1:WP_011842126.1 Length = 327 Score = 149 bits (375), Expect = 1e-40 Identities = 96/305 (31%), Positives = 159/305 (52%), Gaps = 14/305 (4%) Query: 52 LIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMV 111 L++L+ L FG+I +F ++ VGIV TLVI+ GID+S + + Sbjct: 13 LLILLAELAIFGMI-NPRFLRPSSLLFGTSDFVQVGIVAVPLTLVIIAGGIDVSFASTVG 71 Query: 112 LSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLAS 171 L+++ G F +G P LS+ GL GA G +N T++ +L P +VTLG S Sbjct: 72 LAAIAFGIANF-FGLPLPLSLAVGLATGAAAGLLNATIIRLTRLQPLVVTLG-------S 123 Query: 172 NFLYSANETIRAQDISANA-SILQFFGQNFRIGNAVFTYGV----VVMVLLVCLLWYVLN 226 +++S T+ + + A+ + F + F G+ VV ++ +L +L+ Sbjct: 124 LYMFSGAATVLSGVVGASGYEGIGGFPEAFTALGYAQVLGLPMPLVVFLVFAAVLLVLLH 183 Query: 227 RTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQ 286 T +GR V+ +G + EAA+ +G+ V R+ + Y L+GL ALAG L GS G Sbjct: 184 LTRFGRLVFQIGQNAEAARHSGMPVFRVQLVTYVLTGLAAALAGLMLSAYFGSARVDLGS 243 Query: 287 FANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLII 346 + +ITA V+GG S++GG+GS++G + I+G GL++ G Q + L G L++ Sbjct: 244 ATLLPAITAAVLGGASIYGGQGSVLGTIIATFIIGYLQQGLQMSGVPSQISSALSGALLV 303 Query: 347 IAVAI 351 + VA+ Sbjct: 304 LVVAL 308 Lambda K H 0.327 0.141 0.420 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 321 Number of extensions: 25 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 360 Length of database: 327 Length adjustment: 29 Effective length of query: 331 Effective length of database: 298 Effective search space: 98638 Effective search space used: 98638 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory